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Bacterial whole genome sequencing

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https://www.readbyqxmd.com/read/29242835/characterization-of-the-mechanisms-of-daptomycin-resistance-among-gram-positive-bacterial-pathogens-by-multidimensional-lipidomics
#1
Kelly M Hines, Adam Waalkes, Kelsi Penewit, Elizabeth A Holmes, Stephen J Salipante, Brian J Werth, Libin Xu
Previous work suggests that altered lipid metabolism may be associated with daptomycin resistance in Gram-positive pathogens, but lipidomic changes underlying resistance are not fully understood. We performed untargeted lipidomics by using three-dimensional hydrophilic interaction liquid chromatography-ion mobility-mass spectrometry (HILIC-IM-MS) to characterize alterations in the lipidomes of daptomycin-susceptible and -resistant isogenic strain pairs of Enterococcus faecalis, Staphylococcus aureus, and Corynebacterium striatum...
November 2017: MSphere
https://www.readbyqxmd.com/read/29240520/draft-whole-genome-sequence-analyses-on-pseudomonas-syringae-pv-actinidiae-hr-negative-strains-detected-from-kiwifruit-bleeding-sap-samples
#2
Enrico Biondi, Alan Zamorano, Ernesto Vega, Stefano Ardizzi, Davide Sitta, Roberto De Salvador, Reinaldo Campos-Vargas, Claudio Meneses, Set Pérez, Assunta Bertaccini, Nicola Fiore
Kiwifruit bleeding sap samples, collected in Italian and Chilean orchards from symptomatic and asymptomatic plants, were evaluated for the presence of Pseudomonas syringae pv. actinidiae, the causal agent of bacterial canker. The saps were sampled during the spring of both hemispheres, before the bud sprouting, during the optimal time window for the collection of an adequate volume of sample for the early detection of the pathogen, preliminarily by molecular assays, and then, through its direct isolation and identification...
December 14, 2017: Phytopathology
https://www.readbyqxmd.com/read/29239716/pseudomonas-fluvialis-sp-nov-a-novel-member-of-the-genus-pseudomonas-isolated-from-the-river-ganges-india
#3
Sarabjeet Kour Sudan, Deepika Pal, Bhawana Bisht, Narender Kumar, Vasvi Chaudhry, Prabhu Patil, Girish Sahni, Shanmugam Mayilraj, Srinivasan Krishnamurthi
A bacterial strain, designated ASS-1T, was isolated and identified from a sediment sample of the river Ganges, Allahabad, India. The strain was Gram-stain-negative, formed straw-yellow pigmented colonies, was strictly aerobic, motile with a single polar flagellum, and positive for oxidase and catalase. The major fatty acids were C16 : 1ω7c/ 16 : 1 C16 : 1ω6c, C18 : 1ω7c and C16 : 0. Sequence analysis based on the 16S rRNA gene revealed that strain ASS-1T showed high similarity to Pseudomonas guguanensis CC-G9AT (98...
December 14, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29229530/trichoderma-harzianum-mtcc-5179-impacts-the-population-and-functional-dynamics-of-microbial-community-in-the-rhizosphere-of-black-pepper-piper-nigrum-l
#4
Palaniyandi Umadevi, Muthuswamy Anandaraj, Vivek Srivastav, Sailas Benjamin
Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p=1...
November 29, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29227741/new-subclass-b1-metallo-%C3%AE-lactamase-gene-from-a-clinical-pathogenic-myroides-odoratus-strain
#5
Su Xu, Yijian Chen, Zhuyingjie Fu, Ying Li, Guixiu Shi, Xiaogang Xu, Yang Liu, Minggui Wang
Myroides odoratus is a low-virulence opportunistic human pathogen. Infections caused by M. odoratus are not common, but reports are increasing in recent years. The biggest challenge for treatment is its resistance to most antibiotics. In 2015, we isolated a pathogenic multidrug-resistant strain of M. odoratus from a urinary tract infection (UTI) patient's urine sample. To report the experience in managing M. odoratus-related UTI and investigate the genetic mechanism of this carbapenem-resistant strain, we conducted a series of microbiological and molecular studies...
December 11, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/29227468/metagenomic-binning-and-association-of-plasmids-with-bacterial-host-genomes-using-dna-methylation
#6
John Beaulaurier, Shijia Zhu, Gintaras Deikus, Ilaria Mogno, Xue-Song Zhang, Austin Davis-Richardson, Ronald Canepa, Eric W Triplett, Jeremiah J Faith, Robert Sebra, Eric E Schadt, Gang Fang
Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing...
December 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29225701/cytotoxic-escherichia-coli-strains-encoding-colibactin-and-cytotoxic-necrotizing-factor-cnf-colonize-laboratory-macaques
#7
Yan Feng, Anthony Mannion, Carolyn M Madden, Alton G Swennes, Catherine Townes, Charles Byrd, Robert P Marini, James G Fox
Background: Many Escherichia coli strains are considered to be a component of the normal flora found in the human and animal intestinal tracts. While most E. coli strains are commensal, some strains encode virulence factors that enable the bacteria to cause intestinal and extra-intestinal clinically-relevant infections. Colibactin, encoded by a genomic island (pks island), and cytotoxic necrotizing factor (CNF), encoded by the cnf gene, are genotoxic and can modulate cellular differentiation, apoptosis and proliferation...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/29224071/sequencing-of-genomes-from-environmental-single-cells
#8
Robert M Bowers, Janey Lee, Tanja Woyke
Sequencing of single bacterial and archaeal cells is an important methodology that provides access to the genetic makeup of uncultivated microorganisms. We here describe the high-throughput fluorescence-activated cell sorting-based isolation of single cells from the environment, their lysis and strand displacement-mediated whole genome amplification. We further outline 16S rRNA gene sequence-based screening of single-cell amplification products, their preparation for Illumina sequencing libraries, and finally propose computational methods for read and contig level quality control of the resulting sequence data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222102/tracking-the-taxonomy-of-the-genus-bifidobacterium-based-on-a-phylogenomic-approach
#9
Gabriele Andrea Lugli, Christian Milani, Sabrina Duranti, Leonardo Mancabelli, Marta Mangifesta, Francesca Turroni, Alice Viappiani, Douwe van Sinderen, Marco Ventura
For decades, bacterial taxonomy has been based on in vitro molecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species with reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genus Bifidobacterium and identify apparent misclassifications in current bifidobacterial taxonomy...
December 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29219107/molecular-methods-for-detection-of-antimicrobial-resistance
#10
Muna F Anjum, Ea Zankari, Henrik Hasman
The increase in bacteria harboring antimicrobial resistance (AMR) is a global problem because there is a paucity of antibiotics available to treat multidrug-resistant bacterial infections in humans and animals. Detection of AMR present in bacteria that may pose a threat to veterinary and public health is routinely performed using standardized phenotypic methods. Molecular methods are often used in addition to phenotypic methods but are set to replace them in many laboratories due to the greater speed and accuracy they provide in detecting the underlying genetic mechanism(s) for AMR...
December 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/29216271/genomic-and-phenotypic-characteristics-of-swedish-c-jejuni-water-isolates
#11
Anna Nilsson, Cecilia Johansson, Astrid Skarp, René Kaden, Lars Engstrand, Hilpi Rautelin
Campylobacter jejuni is the most common cause of bacterial gastroenteritis. Major reservoirs are warm-blooded animals, poultry in particular, but Campylobacter can also be transmitted via water. In this paper, we have taken a closer look at the biology and potential virulence of C. jejuni water isolates. Seven C. jejuni isolates from incoming surface water at water plants in Sweden were characterized with whole genome sequencing and phenotypical testing. Multi locus sequence typing analysis revealed that these isolates belonged to groups known to include both common (ST48CC) and uncommon (ST1275CC, ST683, ST793 and ST8853) human pathogens...
2017: PloS One
https://www.readbyqxmd.com/read/29212448/from-genomes-to-genotypes-molecular-epidemiological-analysis-of-chlamydia-gallinacea-reveals-a-high-level-of-genetic-diversity-for-this-newly-emerging-chlamydial-pathogen
#12
Weina Guo, Martina Jelocnik, Jing Li, Konrad Sachse, Adam Polkinghorne, Yvonne Pannekoek, Bernhard Kaltenboeck, Jiansen Gong, Jinfeng You, Chengming Wang
BACKGROUND: Chlamydia (C.) gallinacea is a recently identified bacterium that mainly infects domestic chickens. Demonstration of C. gallinacea in human atypical pneumonia suggests its zoonotic potential. Its prevalence in chickens exceeds that of C. psittaci, but genetic and genomic research on C. gallinacea is still at the beginning. In this study, we conducted whole-genome sequencing of C. gallinacea strain JX-1 isolated from an asymptomatic chicken, and comparative genomic analysis between C...
December 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29211769/arsenic-exposure-and-intestinal-microbiota-in-children-from-sirajdikhan-bangladesh
#13
Xiaoxi Dong, Natalia Shulzhenko, Julien Lemaitre, Renee L Greer, Kate Peremyslova, Quazi Quamruzzaman, Mahmudar Rahman, Omar Sharif Ibn Hasan, Sakila Afroz Joya, Mostofa Golam, David C Christiani, Andriy Morgun, Molly L Kile
BACKGROUND: Arsenic has antimicrobial properties at high doses yet few studies have examined its effect on gut microbiota. This warrants investigation since arsenic exposure increases the risk of many diseases in which gut microbiota have been shown to play a role. We examined the association between arsenic exposure from drinking water and the composition of intestinal microbiota in children exposed to low and high arsenic levels during prenatal development and early life. RESULTS: 16S rRNA gene sequencing revealed that children with high arsenic exposure had a higher abundance of Proteobacteria in their stool compared to matched controls with low arsenic exposure...
2017: PloS One
https://www.readbyqxmd.com/read/29209908/purification-and-characterization-of-exo-inulinase-from-paenibacillus-sp-d9-strain
#14
S Jeza, S B Maseko, J Lin
This study intended to purify and characterise exo-inulinase of diesel-degrading Paenibacillus sp. D9. The whole genome sequencing of Paenibacillus sp. D9 revealed to possess the sacC gene that is encoded as exo-inulinase/levanase. This isolate was capable of producing a maximum of 50.9 IU/mL of exo-inulinase activity within 3 days at 30 °C, 200 rpm and pH of 7.0 on minimal salt medium agar supplemented with 1% (w/v) inulin. An exo-inulinase of 58.5 kDa was purified using ammonium sulphate precipitation, HiTrap QFF column and MMC column chromatographies with a specific activity of 4333 IU/mg, 7...
December 5, 2017: Protein Journal
https://www.readbyqxmd.com/read/29207350/mobile-genetic-elements-and-antibiotic-resistance-in-mine-soil-amended-with-organic-wastes
#15
Carlos Garbisu, Olatz Garaiyurrebaso, Anders Lanzén, Itxaso Álvarez-Rodríguez, Lide Arana, Fernando Blanco, Kornelia Smalla, Elisabeth Grohmann, Itziar Alkorta
Metal resistance has been associated with antibiotic resistance due to co- or cross-resistance mechanisms. Here, metal contaminated mine soil treated with organic wastes was screened for the presence of mobile genetic elements (MGEs). The occurrence of conjugative IncP-1 and mobilizable IncQ plasmids, as well as of class 1 integrons, was confirmed by PCR and Southern blot hybridization, suggesting that bacteria from these soils have gene-mobilizing capacity with implications for the dissemination of resistance factors...
December 2, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29197647/genetic-basis-of-chromosomally-encoded-mcr-1-gene
#16
Ruichao Li, Hua Yu, Miaomiao Xie, Kaichao Chen, Ning Dong, Dachuan Lin, Edward Wai-Chi Chan, Sheng Chen
Compared to plasmid-bearing mcr-1, the occurrence of chromosomally-encoded mcr-1 was rare although it has been reported in several cases. This study aims to investigate the genetic features of chromosomally-encoded mcr-1 among E. coli strains and potential genetic basis governing the mobilization of mcr-1 in bacterial chromosomes. The genome sequences of 16 E. coli strains containing a chromosomal mcr-1 gene were obtained and analyzed. Phylogenetic and WGS (Whole Genome Sequencing) analysis demonstrated that mcr-1 was associated with four major types of genetic arrangements, namely ISApl1-mcr1-orf, Tn6330, complex Tn6330 and ΔTn6330 in chromosomes of genetically unrelated E...
November 29, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29196295/quasi-metagenomics-and-realtime-sequencing-aided-detection-and-subtyping-of-salmonella-enterica-from-food-samples
#17
Ji-Yeon Hyeon, Shaoting Li, David A Mann, Shaokang Zhang, Zhen Li, Yi Chen, Xiangyu Deng
Metagenomics analysis of food samples promises isolation-independent detection and subtyping of foodborne bacterial pathogens in a single workflow. Selective concentration of Salmonella genomic DNA through immunomagnetic separation (IMS) and multiple displacement amplification (MDA) were shown to shorten culture enrichment of Salmonella-spiked raw chicken breast samples by over 12 hours while permitting serotyping and high-fidelity single nucleotide polymorphisms (SNP) typing of the pathogen using short shotgun sequencing reads...
December 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29188144/an-efficient-pipeline-to-generate-data-for-studies-in-plastid-population-genomics-and-phylogeography
#18
Brendan F Kohrn, Jessica M Persinger, Mitchell B Cruzan
Premise of the study: Seed dispersal contributes to gene flow and is responsible for colonization of new sites and range expansion. Sequencing chloroplast haplotypes offers a way to estimate contributions of seed dispersal to population genetic structure and enables studies of population history. Whole-genome sequencing is expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among single-nucleotide polymorphisms (SNPs) are lost in pooled samples, and treating SNP allele frequencies as independent markers provides biased estimates of genetic structure...
November 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29188067/isolation-and-characterization-of-leptospira-interrogans-serovar-copenhageni-from-a-dog-from-saint-kitts
#19
Christopher R Larson, Michelle Dennis, Rajeev V Nair, Alejandro Llanes, Andrea Peda, Shamara Welcome, Sreekumari Rajeev
Introduction. Leptospirosis is a zoonotic bacterial disease of global distribution affecting humans and animals. The initial phase of leptospirosis resembles many other febrile illness and due to its broad and biphasic clinical manifestations, selection and implementation of appropriate diagnostic tests can be challenging. Case presentation. This report describes a case investigation of a 14 weeks old male, orphan puppy, presented with generalised jaundice, anemia, weakness, and anorexia. Clinical abnormalities included the evidence of renal and hepatic failure...
October 2017: JMM Case Reports
https://www.readbyqxmd.com/read/29186799/whole-genome-re-alignment-facilitates-development-of-specific-molecular-markers-for-races-1-and-4-of-xanthomonas-campestris-pv-campestris-the-cause-of-black-rot-disease-in-brassica-oleracea
#20
(no author information available yet)
Black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is a seed borne disease of Brassicaceae. Eleven pathogenic races have been identified based on the phenotype interaction pattern of differential brassica cultivars inoculated with different strains. Race 1 and 4 are the two most frequent races found in Brassica oleracea crops. In this study, a PCR molecular diagnostic tool was developed for the identification of Xcc races 1 and 4 of this pathogen. Whole genomic sequences of races 1, 3, 4 and 9 and sequences of three other Xanthomonas pathovars/species (X...
November 24, 2017: International Journal of Molecular Sciences
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